Systems and methods for encapsulation and multi-step processing of biological samples

Abstract

This invention relates to methods and systems for isolation of species in semi-permeable capsules and processing of encapsulated species through series of steps and/or reactions. To produce capsules, first aqueous two-phase system (ATPS) droplets are generated using microfluidics system. Then the hydrogel shell layer is hardened by inducing polymerization. As exemplified in this invention to achieve concentric ATPS droplet formation density-matched PEGDA and Dextran polymer solutions can be used. Once a capsule is formed, its composition can be changed by adding new reagents or replacing out old ones (e.g. by resuspending capsules in desired aqueous solution). The hydrogel shell of semi-permeable capsules can be dissolved at selected step during multi-step procedures to release the encapsulated species. This invention exemplifies isolation of individual cells within capsules and using the encapsulated cells for genotypic and phenotypic analysis. This invention also exemplifies use of capsules in multi-step procedures to perform complex biological reactions.

What is claimed is: 
     
         1 . A method for amplifying nucleic acid of a plurality of encapsulated cells in capsules, the method comprising:
 providing semi-permeable capsules containing encapsulated cells, wherein the capsules comprise an inner phase and a hardened shell, and the inner phase comprises the cells;   suspending the semi-permeable capsules containing encapsulated cells in a lysing reagent;   lysing the cells in the capsules, thereby releasing nucleic acid from the cells in the capsules; and   amplifying the nucleic acid released into the capsules, thereby producing amplified nucleic acid in the capsules.   
     
     
         2 . The method of  claim 1 , wherein the encapsulated cells are bacterial cells. 
     
     
         3 . The method of  claim 1 , wherein the amplified nucleic acid is greater than 0.5 kilobases in size. 
     
     
         4 . The method of  claim 1 , wherein the nucleic acid is RNA and the method comprises converting the RNA into complementary DNA by reverse transcription reaction. 
     
     
         5 . The method of  claim 1 , the method further comprising modifying the nucleic acid from the cells and/or modifying the amplified nucleic acid, wherein modifying includes at least one process selected from the group consisting of adding a poly(A) tail to the nucleic acid, adding indexes to the nucleic acid, ligating adapters to the nucleic acid, digesting the nucleic acid, and fragmenting the nucleic acid.